New sequencing technologies and increasingly dense SNP arrays are generating a flood of genetic data. Sample sizes are increasing and the spectrum of genotyped variation is broadening to include structural and multi-allelic variants. This research will develop improved genotype calling methods that are designed for these data and that use information from large sample sizes and from related individuals in novel and powerful ways. The result will be improved genotype data accuracy which will benefit all research on the genetic determinants of health and disease. PUBLIC HEALTH RELEVANCE: The genetic variants carried by an individual can increase or decrease the individual's risk of heritable diseases such as cardiovascular disease and diabetes. This research will develop new methods and software that improve our ability to identify genetic variants that increase or decrease risk of disease. This research will contribute to the prevention, diagnosis, and treatment of heritable diseases in the United States and throughout the world.